[Genome] TFBS conserved in mouse sequences

[Brooke Rhead]

Hello Mali,

You are correct that we do not have a TFBS Conserved track for any mouse 
database.  A previously answered question on this topic is here:

http://www.cse.ucsc.edu/pipermail/genome/2005-July/008024.html

. . . this answer describes how to use the Conservation track to find 
the syntentic regions between human and mouse.

If you would prefer find the human homologs to mouse accession numbers 
and search that way, I can also tell you how to do that.  Go to the 
Table Browser and select the mouse assembly for which you have accession 
numbers.  Select "group: All Tables" and "table: hgBlastTab".  (This is 
a table of alignments between mouse proteins and human proteins.)  Hit 
the "filter: create" button and paste the mouse accession numbers in the 
"query does match" box.  (This box will actually accept a list of 
numbers.)  Hit "submit" and then "get output".  The 'query' field in the 
result will be the mouse accession that you entered, and the 'target' 
field will be the homologous human accession.

I hope this information is helpful.  If you have further questions, 
please do not hesitate to contact us again.

-- 
Brooke Rhead
UCSC Genome Bioinformatics Group



Mali Salmon-Divon wrote:
> Dear Sir
> 
> I have two questions:
> 
> 1. I want to find specific conserved TF binding sites upstream to
> mouse sequences (I did the same for human sequences). However, your
> mouse database does not contain the TFBS conserved truck (although
> the data exist – you did the comparison for the human database). Is
> it possible to search for TFBS conserved using mouse sequences?
> 
> 
> 
> 2. One solution I thought about is to take the human homologous of my
> mouse sequences and to search the TF binding sites on the human
> sequences. Please advise how I can retrieve the human homologous
> accession numbers from the table browser (using mouse accession
> numbers).
> 
> Looking forward to your answer
> 
> Thanks a lot
> 
> Mali
> 
> 
> 
> Mali Salmon Bar Ilan University, Israel 
> _______________________________________________ Genome maillist  -
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